I think that the best way to achieve this would be to have native mesoamerican kindoms remain independent after the first contact with the west. If western penetration had been peacefull and gradual (i.e. only merchands and missionaries), Christian missionaries might have been welcomed, as they were in China. Their wisdom and practical skills might have been appreciated, even if their religious ideas might have caused some opposition in the court and among the priests.
It is possible that a missionary might have convinced the Aztec/Tarascan/other Court to reform their writting system. The new system would probably have much more to do with the previous mesoamerican one (at least in the shape of the characters) than with latin scritpt, as reformers wouldn't probably favour the introduction of a totally alien form of script. A new system nort too different from the old one might have been accepted without much opposition of conservative priests.
Another possibility (still in this scenario) could be that the Pochteca, the highly developped Aztec merchant class, invent a simpler system after being in touch wohit western merchants. If contact between both word is gradual, Aztects merchands would be more in contact westerns than the high ranking military and religious elite. The Pochteca, as merchands, might have been the first to see the benefits of this new system, and wouldn't be very concern of the religious implicances reforming the system might cause. There would be to systems: the traditional one, used for inscriptions and for religious purposes, and the reformed one, used by merchants.
If we assume the Aztecs remain independent after the first contact with the west in the XVI century, and that they invent a new system (with or without the help of missionaries), this system might survive even if the empire falls eventually under a western power (i.er, in the late XVIII century). The traditional system might disapear with the destruction of the elite, but the reformed one might survived, used by merchands and writers. It might become a symbol of resistance, and might be adopted by the country once decolonisation occurs. (I'm thinking in Korea, whose reformed system, developped in the XV or XVI century, wasn't widely adopted till the XX century).